Season two ended with Charlie running a successful start-up company and the couple reconciling, making most fans happy.

But it sounds like Dunham will now have to do some re-writes for season three after Abbott is no longer a part of the story line.

“They’ve just started work on Season three, and Chris is at odds with Lena,” a source told the Post. “He didn’t like the direction things are going in, which seems a bit odd since the show put him on the map.”

Abbott’s rep confirmed the departure: “[Chris] is grateful for the experience of collaborating with Lena, Judd[Apatow ], and the entire ‘Girls’ cast and crew, but right now he’s working on numerous other projects and has decided not to return to the show.”

Abbott appeared in indie movie “Burma” at SXSW last month and has one film in post-production — but nothing else lined up at the moment.